Patterns of Linkage Disequilibrium across Human Chromosomes 6, 21, AND 22

Vega, Francisco De La

doi:10.1007/978-3-540-24719-7_30

Cited by 2 publications

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“…However, the regions around the classical HLA genes were not found to be characterized by particularly high or low LD in our study. Furthermore, similar patterns of LD were found inside and outside the MHC and probably also exist in other chromosomal regions (De La Vega et al 2003). Primary DNA structure and topology have also been discussed as potential factors promoting recombination (Jeffreys et al 1998, Guillon andde Massy 2002;Jeffreys and Neumann 2002;May et al 2002).…”

Section: Discussionmentioning

confidence: 64%

Patterns of linkage disequilibrium in the MHC region on human chromosome 6p

Stenzel

Koch

et al. 2004

Hum Genet

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Single nucleotide polymorphisms (SNPs) in the human genome are thought to be organised into blocks of high internal linkage disequilibrium (LD), separated by intermittent recombination hotspots. Since understanding haplotype structure is critical for an accurate assessment of inter-individual genetic differences, we investigated up to 968 SNPs from a 10-Mb region on chromosome 6p21, including the human major histocompatibility complex (MHC), in five different population samples (45-550 individuals). Regions of well-defined block structure were found to coexist alongside large areas lacking any clear structure; occasional long-range LD was observed in all five samples. The four white populations analysed were remarkably similar in terms of the extend and spatial distribution of local LD. In US African Americans, the distribution of LD was similar to that in the white populations but the observed haplotype diversity was higher. The existence of large regions without any clear block structure renders the systematic and thorough construction of SNP haplotype maps a crucial prerequisite for disease-association studies.

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Section: Discussionmentioning

confidence: 64%

Patterns of linkage disequilibrium in the MHC region on human chromosome 6p

Stenzel

Koch

et al. 2004

Hum Genet

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“…However, many important questions remain unresolved, ranging from the conservation of haplotype block structures and tagging SNP sets across different populations [Gabriel et al, 2002a,b;Reich et al, 2002;Perola et al, 2002] to the consistency of various block partitioning and tagging SNP definitions and methods [De La Vega et al, 2002;Bafna et al, 2003], and even to the validity of the haplotype block concept itself. To address these questions, it is necessary to develop similarity measures to objectively compare block partitions and tagging SNP sets.…”

Section: Introductionmentioning

confidence: 99%

Haplotype block structures show significant variation among populations

Liu

Sawyer

Mukherjee

et al. 2004

Genetic Epidemiology

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Recent studies suggest that haplotypes tend to have block-like structures throughout the human genome. Several methods were proposed for haplotype block partitioning and for tagging single-nucleotide polymorphism (SNP) identification. In population genetics studies, several research groups compared block structures across human populations. However, the measures used to quantify population similarity are either less than satisfactory or nonexistent. In this article, we propose several similarity measures to facilitate the comparisons of haplotype structures, namely block boundaries and tagging SNPs, across populations. With these measures, we can more objectively compare haplotype block structures and tagging SNP sets between different populations. In addition, these measures allow us to compare the results of different methods for block partition and tagging SNP identification. When we applied these measures to a real data set on chromosome 10 in 16 worldwide populations, we found that in this genome region: 1) haplotype block boundaries vary among populations, with European and some African populations showing similar boundaries but other populations showing other patterns; 2) tagging SNP sets are generally similar for populations with similar haplotype block structures but differ if the block structures differ; and 3) all but one of the block finding methods we tested yield consistent results, although variations exist regarding consistency. Our tentative results show that at least in the genome region studied, it is unlikely that a common haplotype pattern exists for all human populations: many populations, even in the same geographical region, may have different haplotype patterns.

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Patterns of Linkage Disequilibrium across Human Chromosomes 6, 21, AND 22

Cited by 2 publications

References 0 publications

Patterns of linkage disequilibrium in the MHC region on human chromosome 6p

Patterns of linkage disequilibrium in the MHC region on human chromosome 6p

Haplotype block structures show significant variation among populations

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